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Computational Assessments of Scenarios of Change for
the Delta Ecosystem1. Project Purpose
In recent years, two guiding principles have been established regarding the future management of the
Sacramento-San Joaquin Delta. First, Governor Schwarzenegger’s Blue Ribbon Task force
recommended that “the Delta ecosystem and a reliable water supply for California are the primary, co-
equal goals for sustainable management of the Delta” [36], and this principle recently became state law
[14]. Second, fundamental changes in the external forcings (e.g. climate) and physical configuration of
the Delta are inevitable [33,52]. These guiding principles lead to the fundamental question we propose
to address:

How will future changes in physical configuration and climate affect water quality, ecosystem
processes, and key species in the Delta?

In particular, we propose to test the hypothesis that: Climate induced changes in hydrology, sea
level, and local meteorology, combined with new water conveyance structures or increased numbers of
flooded islands, will impact water transport and water quality (e.g. salinity, temperature, and turbidity)
in the Delta. These changes will further influence ecological processes and key species (e.g. primary
productivity, distributions and effects of invasive bivalves, marsh sustainability, contaminant dynamics,
and success of native and alien fish populations). We propose to test this hypothesis by building on the
work of the CASCaDE I project. CASCaDE I was conceived as a step toward developing the
capabilities and understanding needed to assess potential responses of the Bay-Delta ecosystem to
external (climate) and internal (e.g., Delta configuration) changes over the long term. Model simulations
and results from CASCaDE I focused on climate as the primary driver. The approach taken was to link
numerical and statistical models of the major components of the Bay-Delta-River-Watershed (BDRW)
system, representing both physical and biological aspects.

A large part of the effort in CASCaDE I was devoted to numerical model development and linkage,
as appropriate models of several components of the BDRW system were not yet available. In particular,
this resulted in the following new datasets and modeling capabilities:

• A “constructed analogues” statistical downscaling technique was further developed, tested, and
applied to downscale global climate model (GCM) temperature and precipitation [34,13,57], resulting in
gridded daily values of multiple meteorological quantities over California for the 21st century [24]. The
constructed analogues technique was adapted to other variables, including short wave radiation and
humidity over the Bay, Delta and associated watershed.

• A model of water levels at San Francisco, based on empirical relationships [65] and GCM
output, was developed and applied to produce hourly sea-level projections for the 20th and 21st centuries
[13]. A hydrodynamic model was used to propagate these time series throughout San Francisco Bay, and
detailed regional maps of inundation vulnerability were produced [43].

• The California Department of Water Resources operations model, CALSIM
(, was modified to be driven directly by a
hydrologic model of the watershed [42]. The result is a new capability to simulate the response of
California’s freshwater management infrastructure to individual 100-year scenarios of climate change.

• A new modeling approach for hindcasting and forecasting morphodynamic development was
applied to San Pablo Bay [83,84] and Suisun Bay [31,30] by calibrating and validating 3D
morphodynamic models (ROMS and Delft3D) against 150-year datasets of bathymetric development.

• Life history parameters and relationships to environmental factors were established for Corbula
amurensis and Corbicula fluminea, forming a basis for dynamic modeling of benthic bivalves.
• A new approach to calculating phytoplankton production and growth [following 17,18,10,38]
was implemented, tested, and compared to more classical approaches, taking advantage of productivity
measurements and high-correlation empirical relationships specific to the Delta.

• A new graphical and mathematically simple conceptual model of the general relationship
between algal biomass, residence time, growth rate, and loss to grazing was developed. At the heart of
this conceptual model is a simple index capturing 1) whether a habitat is algal growth dominated or loss
dominated; and 2) how phytoplankton biomass will respond to changes in residence time [50].

• A conceptual and quantitative model for predicting food web response to changes in Se exposure
was developed from local data and a comprehensive analysis of the global literature [54,64]. The time
series of Se concentrations in C. amurensis in Suisun Bay was extended to present, spanning a range of
hydrodynamic conditions critical for model refinement [64] and hypothesis testing [77].

• Outputs from many of the above models were used to assess habitat conditions for selected fish
species, including salmonids in the Sacramento Rivers, Sacramento splittail in Yolo Bypass, and delta
smelt in the Sacramento-San Joaquin Delta.

In CASCaDE I, several of these new modeling capabilities were linked and applied to evaluate the
response of the BDRW system to multiple climate-change scenarios that spanned a range of projected
futures. This resulted in projections of hydrologic responses, sea-level-rise impacts, changes in sediment
supply and geomorphology, and fish population responses under projected climate change. These
scientific results and their implications for our conceptual model are discussed in the next section. Links
to relevant publications and data can be found at the CASCaDE Project web site: In CASCaDE II, we intend to build upon, update, and extend the work of
CASCaDE I with coordinated efforts toward the following objectives:

1. Generate updated scenarios of meteorological forcings, watershed flows and stream
temperatures, and downstream sea levels based on new GCM outputs corresponding to the upcoming
Intergovernmental Panel on Climate Change 5th Assessment Report, as these data become available.

2. Develop and apply a new model of sediment transport in the Bay-Delta watershed to better
understand upstream sources of sediment, and to project future patterns of sediment transport into the
Delta under scenarios of climate change.

3. Apply a new model of Bay-Delta hydrodynamics and sediment transport, Delft “UNSTRUC”, to
evaluate key quantities such as residence time, salinity, water temperature, and turbidity under scenarios
of climate change and alternate physical configurations of the Delta.

4. Enhance UNSTRUC to include capabilities for simulating coupled phytoplankton dynamics and
non-native clam distribution, biomass, and grazing rate, and extend the evaluations in (3) to include
these quantities. Use output from these new coupled models to support contaminant modeling.

5. Include a peat accretion modeling component to evaluate the survival of existing and restored
marshes under climate change.

6. Incorporate results from (1)-(5) to refine and update assessments of survival likelihoods for
native and alien fish populations, including species not considered in CASCaDE I.

Linking the capabilities developed in CASCaDE I with the new capabilities proposed in CASCaDE
II will enable a more complete and accurate evaluation of the response of the BDRW system to updated
climate change scenarios. Importantly, the incorporation of a robust hydrodynamic model of the Delta
capable of simulating key physical and biological processes will also allow the evaluation of ecosystem
impacts of scenarios of Delta configuration change (alternate freshwater conveyance infrastructure,
flooded islands), in combination with the climate change scenarios. These are the goals of CASCaDE II.

Specific scientific questions relating to the scenarios of climate and Delta configuration changes to
be addressed in CASCaDE II include:

• Which downscaled meteorological changes are robust across climate models? Which are not?
What does this imply about projections of hydrologic and other downstream changes?

• How will upstream hydrologic changes combine with sea level rise to affect inundation patterns
in the Delta region? How will peak stage change relative to levee heights?

• What is the likely trend of the future sediment yield from the Sacramento River? Has a post-dam
equilibrium been established?

• What and where are the major sources in the Sacramento River watershed that supply sediment
to the Delta? How might the rates of supply from these sources change due to climate change?

• What are the dominant suspended sediment (SS) transport processes within the Delta? How will
these change under the scenarios considered?

• Will rates of vertical peat accretion in various Delta marshes be high enough to sustain marshes
under conditions of future sea-level rise or will certain marshes eventually be drowned?

• Will increased shallow habitat significantly influence propagation of tides (as suggested by J.
Burau, USGS)? How will transport processes through the Delta be affected?

  • Under which scenarios will the Delta be more susceptible to salinity intrusion?
  • How do the distributions of Corbula and Corbicula change with salinity distribution under the
    scenarios considered? How does the change in grazer biomass distribution affect phytoplankton
    biomass and contaminant bioaccumulation and availability to higher trophic levels?

• How will future changes in hydrodynamics (e.g. residence time, stratification), water clarity,
grazing, and distribution of habitat depths affect phytoplankton biomass and productivity?

• How do changes in residence time, potential sources of Se (San Joaquin Valley, refineries, local
streams) and composition of suspended particulate material (phytoplankton and inorganic particles)
impact Se accumulation in Corbula amurensis in Suisun Bay and how could those relationships change
with different scenarios of climate and infrastructure change?

• What are the likely effects of flooded island and "alternate conveyance" scenarios on fish
populations? How will key habitat attributes for fish (e.g. temperature, turbidity, salinity) change in
response to the combination of a changing climate and physical configuration?